Another issue: You will have huge PA/IP issues in the early years with pitchers/hitters that did both but the SIM won't actually allow to play both. Even if you avoid the PA/IP issues, you definitely have issues with the realism of the replay pre-1901 because of this.
Also how you would handle stuff like the Federal League and some of the extra leagues in the 1800s comes to mind... there definitely isn't a "3 leagues" format or a "1800s" format (likely because the 1800s was crazy and unregulated) -- you partially mention this, but the issue in those years is imho even deeper than it looks. As for 1900, your best bet might be a "double replay" -- 8 team AL, 8 team NL, identical teams, different owners, and don't really care about the WS result...
I'm honestly also not sure of the point of replays. While they won't replay the same, they'll replay in a similar enough manner as to not be hugely relevant -- as you said, a 60-win team isn't going to suddenly win the league. So I'd have to say it's not interesting. I don't need to see <random 100 win team> crush <random 60 win team from the same year>.
Your best bet might be to do a replay that invokes "time travel" players to balance out the competitiveness of the team -- possibly with a number of players coming in based on the original winning percentage, or a salary limit applying just to it based on that... something along these lines... thejuice6 has run several leagues doing free agent ideas this sort of way, but not with all of a single season's rosters being played... on the other hand this does spoil it being a true replay. But you might actually sell the league.